Intraoperative frozen section (FS) can be reduced during thyroid lobectomy according to the results of fine needle aspiration (FNA). We evaluated the role of intraoperative FS in thyroid nodules with different diagnostic categories of the Bethesda System for Reporting Thyroid Cytopathology by FNA. This retrospective study included 1,235 nodules collected via thyroidectomy with both preoperative FNA and intraoperative FS at the Second Affiliated Hospital of Zhejiang University School of Medicine, from January 2011 to January 2014. FNA cytological diagnosis was classified into six categories, based on the Bethesda system. The diagnostic findings of FNA cytology and FS histology were compared with the final histological results. 189 nodules were benign. The remainder were malignant. FS diagnosis was more accurate than FNA diagnosis for nodules classified as Bethesda Categories II, III, and IV (P < 0.05). However, the accuracy of FNA diagnosis in nodules assigned Bethesda Categories V and VI was significantly higher than that of FS (P < 0.05). FS appears be beneficial for thyroid nodules classified as Bethesda categories I through IV. FS may not be necessary in nodules diagnosed as Bethesda Categories V and VI.